This Not So Mortal Coil
by YunaDax
Summary: What if it were the real Elizabeth on the planet in This Mortal Coil, and not a clone?
1. Chapter 1

Title: This Not So Mortal Coil  
Author: yunadax  
Rating: PG-13  
Word Count: 3247 (so far!)  
Prompt: KrisRussel on GateWorld – What if it was the REAL Elizabeth in the jumper that went down in This Mortal Coil

Summary: What if it was the REAL Elizabeth in the jumper that went down in This Mortal Coil?

Spoilers – This Mortal Coil

'It was easier this way', she had told herself as the blatently lied to her old 2IC. She wasn't a clone, well not completely anyway, yet she wasn't Elizabeth Weir either. The Replicators had screwed with her mind so much in the past few months she had almost lost all sense of self, reduced to a trembling shell that had been 'reprogramed' more times than she could remember in order to subdue her human tendancies and her strong willpower. Every time she had woken up on the same bench in the same empty lab, not daring to believe anything that her senses told her. This time however, things were different.

Sometime during her last 'reprogramming' she had been taken by the rebel Replicators and trust into a simulated Atlantis in order for them to learn from her vast Ancient knowledge how to ascend. While it was something she was acutely interested in, the thought of staying alive usually overpowered any thoughts of trying to ascend to escape the hell her life had become since she'd been taken. She met up with a cloned Atlantis team, completed with a cloned Dr Keller, heck even down to Chuck in the control room. As they began to work things out they were tossed in a jail cell, apparently too dangerous to continue without being 'reset'. It was then the replicators attacked, and Elizabeth had begged for them to be released so they could make a difference. Thankfully the Keller Replicator had done just that, giving them the tracking system from a core of one of the Replicator ships, before allowing them a puddlejumper to escape the destruction of the pseudo-Atlantis.

After catching a lift on the hull of a Replicator ship and stealing another from the Replicator homeworld, the team ended up on M34-227, and bumped into Major Jordan. Perfect.

" I'm not Elizabeth. Well, not the Elizabeth you knew. I have all of her memories and all of her thoughts – everything that makes her me. But I'm a duplicate. I was created by a faction of the Replicators as a means to attaining ascension. " She lied, her face a mask devoid of all emotion. If he knew she were dead, he wouldn't keep trying to rescue her, risking his own life and those of whoever he brought with him. She would never be the same Elizabeth anyway, and it would be easier for him to beleive she were dead.

An arrangement was made for the 'real' Atlantis team to come to M34-227 to meet up and discuss the tracking device, and as expected the McKays got along not only famously, but irritatingly so. They bustled each other out of the way of the one set of equipment available to them, both as eager as the other to get into the guts of the tracking device.

Elizabeth decided to take a walk with the 'real' John to solidify her case with him, claiming that the Replicator Keller had told her that her original was dead. Not that there was any way for John to rectify her statement, so he would have to take her word for it. He made a good argument though, encouraging her to bring her team back to the 'real' Atlantis and make a life for themselves there. She could feel her composure crumbling, her mind as twisted as the Replicators had made it wanting to desperately go back to her old life. Yet she couldn't, and wouldn't put John through that. He deserved so much more than a leader and a best friend who was part replicator.

Ironically it was then that Oberoth's Replicators decided to attack, sending down streamed of weapons fire onto the surface of the planet as well as blocking the Stargate to prevent their escape. Her first priority was the lives of the 'real' Atlantis team, she couldn't let any harm befall them, not when 'her' team were merely clones. They planned a diversion, taking the puddlejumper and drawing the Replicator's attention and fire. A blast hitting the rear of the jumper sent them all sprawling inside the small cockpit, then careening out of control towards the forest below. The impact sent them flying, and for a moment, Elizabeth knew that this pain was real, not something that the Replicators were trying to trick her mind into feeling. Her leg was twisted underneath her, the bone splittered into a thousand peices by the impact and a trickle of blood oozed from where her head had connected with the bulkhead. Pain coursed through her body, the nanites within her repairing the damage even as she lay in agony. Footsteps approached the jumper and she feigned unconsciousness, which wasn't particularly hard as she was teetering on the verge of it. The ramp descended and a team of Replicators approached her, probing her mind to see how alive she really was. She blocked them, emptying her consciousness of anything other than emptiness, hoping it would fool them. 3 more Replicators entered before John swivelled round, pulling a weapon on them. They fired first, and he slumped forward, his face resting on the consol of the jumper. They fired again and he vanished entirely, ceasing to exist in anything but her memories. They repeated the process with Ronon, Teyla and Rodney before turning towards her, their weapons trained on her crumpled body.

" This is Oberoth, return to the ship" Came the mental transmission that Elizabeth picked up between the Replicators, and they thankfully left her, beleiving she was indeed dead and not worthy of wasting their time to disintergrate. Another volley of weapons fire from orbit heralded the departure of the footsoilders, leaving her very much alone in the forest. A blast hit the puddlejumper and her mind once again shut down.

" Colonel we have to go back there to see if they made it" John implored the next day to Colonel Carter, knowing full well the Replicators would have left by now if the other team were dead. If they had escaped, the Replicators would be hunting them and a cloaked jumper could avoid their detection.

" You're sure the Replicators would have left?" Carter asked, tapping her laptop idly as John pleaded his case.

" Sure enough that if they were still there a cloaked jumper would easily slide under their noses" John replied, injecting his voice with as much 'please believe me' as he could.

" Alright, but if you hit ANY resistance, I want you all back here ASAP" Colonel Carter aquiesed, unable to hold her smile as John all but bolted out of her office. She knew this was important to him, if they other team was dead, it would provide closure, if they weren't, there was the possibility of a rescue, and she would cross THAT bridge if and when it appeared in front of her.

Within 20 minutes the jumper descended through the ceiling of the gateroom, Carter wishing them 'Good luck' as they vanished through the event horizon. Seconds later they were on the planet, cloaked and invisiable to both the naked eye and most sensors. Thankfully the Replicators were nowhere in sight.

" I've found the jumper... its about 30 klicks northwest" Rodney reported, tapping his tablet to gain more accurate information.

" Any lifesigns?" John asked.

" None yet... but they were replicators remember" Rodney remarked.

" The others were, but something was... I dunno... different about Elizabeth. I don't think she was like them" John said sadly, knowing in his heart that all they would be finding would be bodies.

They flew in silence for a few moments more before the jumper appeared on the forest floor, a gouge of destruction marking the path it took to end up half submerged in greenery and soil. John eased their jumper to rest nearby, lowering the ramp and holding his weapon ready in case anything unexpected was lumped upon them.

The other jumper was a mess, twisted metal and componentry spread amoungst the trees and shrubs. The basic hull was intact, but that was about it. The ramp bad been partially lowered, but the inside was pitch black, giving no insight as to what they might find inside. Outwardly John was impassive, his expression neutral and his actions deliberate as he moved to check the interior of the jumper, inwardly his heart was in his throat, his stomach twisting in so many knots he thought he might be violently ill at any moment. The next few moments would determine everything.

Flipping on the light on his P-90 he gingerly made his way inside, finding a plethora of shrapnel imbedded in every soft surface within the rear compartment. Then he saw her, crumpled in a heap on the floor, her face clearly visiable but relaxed, one of her legs twisted and broken beneath her.

It was then he noticed her chest rise and fall ever to imperceptibly, the exhalation of air ruffling a small strand of hair that had slipped across her face.

He crept forward, weapon still raised and dropped to one knee, pressing his fingers to the side of her throat in the age old tradition of checking a persons vital signs. He almost lost all coherent thought when he felt it thrum beneath his fingers.

Wait a minute.. did replicators have a pulse? His mind raced against the posibilities and came up with a negative.. why would a replicator need a pulse?

" Elizabeth?" He called her name softly, the hand not on his weapon gently sweeping the hair from her face. She stirred a little under his touch.

" John?" She asked, not quite opening her eyes just yet.

" Yeah.. who else would risk their ass for you, even if he'd be lied to?" He quipped, his relief evident in his voice.

" I hurt like hell" She admitted, grimacing as the pain in her leg became evident. The nanites within her still worked to repair the injury, but she had been so badly damaged both in the crash and the weapons fire afterwards they hadn't finishing repairing everything just yet.

" You're the real Elizabeth aren't you?" John asked quietly, digging through the small medkit in his vest to find some painkillers.

She opened her eyes, the apology clear within their green depths.

" I'm sorry John, if you'd just moved on then you wouldn't be here risking your ass for me" She admitted, tears beginning to glisten.

" God Elizabeth..." John swore, pulling out a small vial of morphine and loading a medipen with it. He injected her with the medication, easing her pain whilst be made contact with the rest of the team waiting patiently outside the jumper.

Part replicator or not, she was going home.

Three days later Dr Elizabeth Weir was released from the infirmary, the nanites in her body finally having repaired her splintered leg with the aid of some surgery. The bone was pinned back together and the muscles were already repairing themselves, allowing her to walk with only a slightly noticeable limp until the nanites finished their repairs.

As she wandered through the corridors she had the distinct feeling that she was caught between worlds. While people seemed happy that she was back she could see the uncertainty in their eyes, and the two marines shadowing her didn't overly sell the whole idea that she was 100% normal. Thankfully Teyla seemed to be her constant companion, something that Elizabeth was more than thankful for. She had always respected Teyla's ability to put people at ease and to allay their fears, and sometimes the softly spoken words of the Athosian put her trouble mind at ease more than she realised. The one thing that concerned her more than the Atlantis team accepting her back into their ranks was the disappearance of John Sheppard. Whilst she knew he was in the city still and not 'lost' per say, it was more than he seemed to be avoiding her, distancing himself from her. Dr Heightmeyer assured her it was merely his way of coping with her return, but Elizabeth had a strange feeling there was something more going on. Something was weighing on John's mind and he wasn't going through his normal channels to alleviate it. He would normally have cornered her in her office, or on the balcony if he needed to get something of his mind, but the sinking realisation that it was no longer HER office, and the balcony was more likely Colonel Carter's more than hers made her realise that things had changed since she left.

Elizabeth had spent a great deal of time working with Colonel Carter and Dr McKay since she'd returned from the planet, mainly trying to work out a way to neutralise the nanites without killing herself in the process. Until that was done the guards would be her constant companion, and whilst she didn't appreciate being treated like a prisoner in her own city, she understood the reasons why.

As she arrived back in her old quarters, she found some things almost as she'd left them. Some of the personal belongings lay neatly stacked in boxes along one wall, as though someone had begun to pack them up before getting called away for something urgent. The guards thankfully remained outside her door, allowing her a modicum of privacy.

" I am sorry that we started packing your belongings" Teyla apologised, picking up one of the boxes and placing on the bed for Elizabeth to start unpacking.

" It's ok Teyla, I honestly didn't think I would be coming back myself" Elizabeth replied quietly, unable to take her eyes of the items in the box. Uniforms, casual clothes, knick knacks that she'd had around her quarters were all carefully folded and packed with great care and reverence.

" Who did this?" Elizabeth asked, picking up the jacket of her old uniform, complete with the Atlantis pin still attached to the lapel that designated her as the leader. She hadn't worn that jacket in years, preferring now the black jacket and pants that were way more comfortable.

She saw Teyla hesitate, before gathering herself to reply.

" John did, he would not let the rest of us aid him" Teyla replied softly, casting her eyes towards the box as Elizabeth unpacked things one at a time.

" I'm worried about him, it's not like him to avoid me" Elizabeth couldn't help but admitting out loud, how was it that Teyla could always get her to say what was really troubling her without evening trying?

Again, Teyla paused.

" He... feels responsible for not rescuing you sooner" The Athosian answered, carefully choosing her words.

" He's beating himself up over this isn't he?" Elizabeth knew John almost as well as John knew himself. She knew his ability to punish himself when he thought he had failed someone.

" He is, and he will not listen to anyone, not Colonel Carter, Ronon nor myself" Teyla admitted honestly.

" Could you ask him to see me? As a friend?" Elizabeth asked before she even knew the words were out of her mouth. 'Where did THAT come from?' she criticised her mind in the milliseconds after she'd spoken.

" I can try, but I do not guarantee he will in his current state of mind" Teyla finished before turning and head out of the room, leaving Elizabeth alone with her troubled thoughts.

She unpacked her belongings, setting each item back in its original place before stacking the boxes to one side to be disposed of in the morning before wandering over to the long window and staring out in wonder at the city she never thought she would see again. She had no idea how long she simply stared at the glowing lights emanating from the buildings that surround the one where her quarters were located, before a knock on the doorframe startled her.

" Come in" She called, turning to face the intruder. John walked through the door, his face a mask of impassiveness, not expressing a single emotion. He was hiding from his own feelings, burying them as though nothing had happened, but refusing to even acknowledge her presence since she had returned.

" You wanted to see me Dr Weir?" He said officially, his stance rigid and stilted.

" John, I just wanted to say thank you, and that you aren't responsible for what happened" Elizabeth started, her expression honest and open. Darn it why was he making this so hard?

" It's my job to protect you, I failed" John replied stoically, his expression unyielding.

" John, there was nothing you could have done..." Elizabeth started to explain.

" Damnit Elizabeth, I left you behind in the hands of the _enemy_!" John's anger exploded and Elizabeth resisted the urge to back-peddle away from him. He was almost shaking in self loathing.

" John, I survived, why can't you see that?" She raised her voice, not quite shouting, but loud enough to break through the self-loathing echoing around his mind.

" I should have tried harder, I should have gone back sooner" John repeated, almost ignoring her words entirely.

" And done what? Get caught yourself? John it wasn't pleasant by any means what they did to me, and I'm thankful that I was the only one they had to screw with. I couldn't bear having you go through the same thing." Elizabeth said quietly, her anger subsiding as she finally started to get through to him. Had she just admitted the one thing they had both promised never to acknowledge in public? Had she just stepped across the line they had be toeing for so long?

John was quiet for a moment, his expression conflicted as he digested this new information.

" If I'd gotten there sooner, they wouldn't have tortured you" He stepped forward, grasping her by her shoulders " I should have prevented it from happening in the first place" He implored, meeting her eyes for the first time. She saw the anger and torment hidden in their depths, the pain and self-loathing evident only to those who really knew him.

" No-one could have prevented it, and for what its worth, the mission was worth it" Elizabeth retorted gently, unused to seeing him this open and vulnerable.

" You're worth more than any mission" John said with an intensity that shock Elizabeth to her core. The arms slipped from her shoulders to wrap around her back, pulling her forward into an embrace she had no hope of recovering from. She melted against his strong frame, her chin tucking in towards his neck as his body pressed against hers. She drank in his scent, the hint of aftershave mingled with the unique scent that was simply John Sheppard. Despite all that had happened, for those few moments she was enfolded within his arms, she could forget the horrors of the past few months and simply be herself.


	2. Chapter 2

The next few days were a blur of meetings and interviews for Elizabeth. Thankfully this time John keep close at hand, with Teyla always nearby when he wasn't. Colonel Carter was gracious enough to allow her to work as an Ancient translator and negotiator until the IOA decided what they wanted to do with her. She couldn't return to Earth in case the Replicators tracked her there directly, so Atlantis was the safest option for both Elizabeth and the greater human population. Talk about feeling like a 'Typhoid Mary' . When she wasn't being grilled about her time under the replicator's control she was in the lab with Rodney and Dr Keller, both trying to work out a way to neutralise the nanites within her body without killing her in the process. In the interim Rodney had decided that setting up a dampening field around Atlantis was the easier and more immediate option, thus blocking any signals that might try and 'reintegrate' Elizabeth or tamper with her nanites programming. Eliminating the nanites would have to come later, or at the very least reprogramming them to only effect essential repairs on her body and nothing else.

3 days after she had returned Elizabeth dragged herself back to her quarters, her mind numb from constant bombardment for information and her body screaming at her to either exercise it to work her stiff muscles or let it sleep. She had noted a physical effect when Rodney had initiated the dampening field, her body aching with a tiredness unlike that which she had ever felt before. Dr Keller assured her the nanites would adapt and she would feel normal again soon, but in the meantime to take it easy.

She opted for a light yoga session with Teyla, the Athosian woman never seemed far from her side and always wanting to offer a ear to air her frustrations with. The yoga mats were pulled out from their storage cupboard and laid on the floor, the two women falling easily into the rhythm of the workouts they used to practice on a regular basis before Elizabeth had been taken. They stretched in a comfortable silence, until the doors opened revealing a rather startled John Sheppard.

" I.. umm... I can come back" John stuttered, seeing both Elizabeth and Teyla in a folding split pose, folding their upper bodies over endlessly long legs. The colour rose in his cheeks and Elizabeth couldn't help but chuckle.

" It's ok John, we're almost done" Elizabeth smirked, unravelling herself and getting to her feet to finish with a few of the easier poses. John plonked himself on the bed to watch, trying to emulate some of their movements with a comical expression on his face.

" You are intolerable" Teyla remarked with a friendly slap on the shoulder she gave up trying to concentrate on her poses and caught John imitating her out of the corner of her eye. She bade Elizabeth farewell and departed, dropping her yoga mat into the storage cupboard near the door as she left.

" I didn't know you were that flexible" John remarked, impressed by her ability.

" I didn't know you could blush that colour" She retorted, rolling up her own mat and stowing it for later use.

" Takes years of practice" John quipped, flopping down again on her bed. He seemed to be infinitely more comfortable around her since their conversation which had ended up a rather cosy embrace a few days ago, almost as though he'd crossed a line in his mind and wasn't that worried about it anymore. Elizabeth however whilst acutely aware of his change in demeanour, but it was somewhat overwhelmed by the grilling by every man and their dog since she had returned. Now though in the privacy of her quarters with only John for company, she mulled over the change.

John quirked an eyebrow at her sudden seriousness, her expression conflicted as she stared out the long window in her quarters to the city beneath.

" Penny for your thoughts?" He asked gently, rising from the bed and standing close behind her. His hands found their way to her shoulders and began massaging the tense muscles that hadn't quite been released by her yoga workout.

" I was just thinking..." Her voice trailed off, her eyes drifting closed as his fingers worked their magic on her shoulders.

" About?" He prompted after a few minutes, knowing she would be having a hard time concentrating.

" Us...well you more specifically" She finally answered, turning around so that she was facing him. " What changed?"

" Well there's the fact that you technically aren't my boss anymore, and you aren't military, so there's no rules or protocol preventing an... US" John said carefully, choosing his words for maximum effect without sounding like a desperate teenager.

" Well there is that" Elizabeth retorted, honestly not having had the time to consider that little detail since she had returned.

" I don't want to rush things, I just want you to know I'm here for you, and I'd like there to be an 'US' when things settle down " John explained, his hands returning to her shoulders as if to emphasise his point.

She was quiet for a while, her face a mixture of bliss and conflict. He could almost see her mind weighing up the pros and cons of his words before closing down completely as his fingers moved of their own accord into her hair. A sigh of contentment escaped her lips and he took it as a positive sign. Against his better judgement and his self-imposed sanction to take things slowly, he leant forward and brushed his lips to hers, the fleeting contact enough to make her snap her eyes open in surprise.

He immediately retreated, fearful that he'd once again overstepped the line before a hand on his stopped him.

" Please don't" She said quietly, her fingers around his wrist to prevent him from moving further away. " You just startled me... I wasn't expecting that"

Her words sounded odd even to her own ears, tinged by why.. hope.. expectation, a dash of fear perhaps?

He changed tactic allowing his arms to drop to his side in a somewhat innocent matter.

" You don't wanna know how long I've been wanting to do that" He quipped, quirking an irresistible smile at her before reaching and this time grabbing of her wrists.

" Lie down, I'll give you a back massage" He said, indicating for her to lie front first on the bed. She hesitated for a moment and he caught on to her expression.

" I promise I'll behave, you've been through a lot in the last few days, nanites or not you need to relax... besides.. my back rubs are famous in many college dorms" John retorted playfully, pulling her towards the bed. She followed him and did as he instructed, wriggling out of her shirt whilst he tactfully looked the other way. Flopping belly down on the bed and grabbing on of her pillows she tried not to remind herself she was now half naked in front of John Sheppard as she cleared her throat to catch his attention.

The sound of a bottle being pulled from his pocket and a small amount of liquid being poured onto his hands caused her to glance behind her, keeping care to keep her front tactfully covered.

" Massage oil? Where on Earth did you get that from?" she questioned as the lavender scent reached her noise.

" The massage therapist who works with Dr Heightmeyer.. she recommended I get you to relax" John remarked, giving her a look that said ' lie down and don't fall asleep on me'.

Elizabeth took the hint and resumed her position on the bed, covering the intake of breath and John carefully undid the clasp of her bra and slid the straps down her arms. Her skin tingled with his touch and she desperately hoped he couldn't see the colour rising in her face. Damnit she hadn't blushed like this since she was a schoolgirl.

Ever the gentleman Sheppard began his massage, forcing his body to behave as he kneaded the knotted muscles in her back and shoulders. He felt her body begin to relax under his touch, her breathing evening out as she succumbed to the sleep that had been eluding her for the last several nights. He knew she'd been plagued with nightmares, he'd seen the dark circles under her eyes every morning before a healthy slathering of makeup hid any trace of them.

He continued for as long as his hands would hold up, hoping that she was slip into a deep healing sleep and remain that way for a while. He covered her with a blanket, and kicked off his own shoes and claiming what was left of the bed to himself. So it wasn't exactly the way he had envisioned their first night together, but it was a start nonetheless, and he was more than happy with that.


	3. Chapter 3

She slept well that night, her mind quiet and her body relaxed for the first time in what seemed like forever. The early morning light of dawn cast her quarters in an orange/pink glow, highlighting the ancient architecture and the odd personal touch she had embellished her quarters with. She rolled over, content to sleep for another hour before getting up for her first appointment at 1000hours, when her body connected with something soft and yielding lying next to her.

" Mpppffhhh" The body mumbled incoherently, obviously still fast asleep and not wanting to be woken quite yet.

Her eyes snapped open this time, taking in the mass of unruly black hair peeking out from one of her blankets. For a moment she froze, wondering just how much she must have had to drink to completely forget sleeping with someone.. till she realised he was still fully clothed... and he was John Sheppard.

The memories came crashing back to her, shattering the early morning calm that had settled in her mind. The capture, her rescue, the endless meetings and interrogations, and the massage. OH.. the massage! She must have fallen asleep during it, considering she was still topless, but draped in a warm and comfortable blanket.

John must have felt her eyes on him and he cracked an eye open, peering at her over the small mountain of blankets and pillows.

" G'morning" He mumbled, watching the series of emotions flicker across Elizabeth's face one at a time as her mind obviously caught up with her current state of undress and the fact that she wasn't alone.

" Good Morning" She replied, her voice hoarse from sleeping. She seemed to be at a loss for words, her mouth opening and closing several times uselessly before she bothered even trying to form words.

" Don't worry, I behaved myself.. you feel asleep while I was giving you a back rub and I wanted to make sure you actually slept through the night" John explained easily, rolling onto his back and flinging the blanket back. He sat up and stretched, stretching his arms high above his head and rolling his shoulders.

Elizabeth sat up as well, dragging the blanket with her to remain covered before searching around for her top. She found it still rumpled on the bed covers, and John tactfully turned his back while she slipped it over her head.

" I take it you slept better?" He asked as she was once again fully dressed.

" Yeah.. thanks. The back rub really does work miracles. Scuse me... I need a shower" She gave him an honest smile, crossing the room to her bathroom before closing the door and running a hot shower. The hot water felt like heaven against her skin, focusing her mind and revitalising her body. 20 minutes later she emerged in a fresh set of clothes to find John had procured breakfast from somewhere and was now sitting quite happily munching his portion at her desk.

" You know you really shouldn't skip breakfast...." John admonished at her surprise, gesturing for her to come over and join him. She dragged a spare chair over and sat down opposite him, taking in the wafting aroma of fresh toast, juice and a bowl of cereal. Ok so it wasn't bacon and eggs in bed, but it was light, tasty and healthy, and she honestly appreciated the effort.

" Since when have you become my keeper?" She asked with a grin, adding some butter and jam to one of the slices of bread before pouring herself a cup of coffee.

" Since you got back.. and since you started talking about an 'US'" John quipped, scooping up the last of his cereal. " Besides, since the IOA and Rodney have been asking way too many questions and running far too many tests on you to be healthy, I thought you might appreciate some TLC" He added, slurping the last of the milk from his bowl and sipping his coffee.

His words rang true with Elizabeth, and she paused in eating her toast for a moment.

" I do appreciate it John, honest" She said with a smile, enjoying the attention he was lavishing upon her.

" well then it shall continue" John said with a flourish, pinching a corner of her unfinished toast and popping it into his mouth.

" Hey!" She retorted as she tried to grab the toast back again.

" You snooze you loose! Besides.. if I'm doing all this TLC.. I gotta keep up my strength" he smirked, grinning foolishly at her. He honestly hadn't felt this carefree in a very long time and was quite enjoying it.

" Can I rescind that TLC comment if it means you're gonna flog my breakfast?" Elizabeth snarked, protectively holding her bowl of cereal close to her to protect it. She couldn't help but giggle at his antics, the bubbly sound music even to her own ears. How long had it been since she'd laughed?

Ten minutes later she had finished her breakfast and John had departed back to his own quarters for a shower and change of clothes before heading off to his first mission briefing. Elizabeth was due to spend another undoubtedly exhausting day with the IOA and the science teams, full of questions and being prodded with more scientific and medical equipment than she would ever care to lay eyes on again.

Six hours later she returned to her quarters feeling sore and sorry for herself, emotionally and physically drained from her ordeal. She flopped onto her bed, letting the firm mattress support her tired body as she closed her eyes for a few moments of peace and quiet. The questions with the IOA had achieved quite a bit, truth be told. She would officially be still listed as MIA back on Earth, since until they could come up with a permanent solution regarding her nanites she would never be able to set foot on her home planet again. To that end she would be working as the expeditions negotiator and translator, but forced to remain in the city at all times. These walls would become her prison until Rodney and Dr Keller could neutralise the nanites or remove them completely, and although it didn't bother her too much, she knew it would in the future.

A knock on her door and the swish of it opening before she could even open her mouth drew her attention away from her troubles and back to the present. John stood leaning against the doorframe, just enough to let the door slide closed behind him.

" Rough day?" He asked, taking in her expression and her utter.. floppiness.

" Yeah you could say that" She grumbled in reply, rising up on her elbow. " I can't ever leave Atlantis"

" Well that would suck... however it means you can't ever escape me" John quipped, unable to resist the urge to take a run-up then a flying leap to land beside her on the bed. She was nearly launched as the mattress recoiled, causing her to once again giggle at his antics.

" How come you always know how to make me laugh?" She asked between giggles.

" I dunno.. just do" He smirked, making a show of getting comfortable on her bed. " Although.. I wish this place had room service.. I would never leave then!"

" Room service.. pfft... although it is getting late.. is the Mess still serving dinner?" She questioned, nailing him with a semi-serious glare before pulling him up into a sitting position.

He glanced at his watch and nodded his head

" Should be... although dinner's already been served for two hours, so I'm not sure if Rodney's left anything" John mocked, getting to his feet and straightening his shirt. " After you Mi-Lady" he said with a deep bow, gesturing towards the door.


	4. Chapter 4

Three weeks later Elizabeth was holed up in her new office translating some new Ancient text that one of the teams had discovered recently on their travels. Whilst her new role as translator/linguist / negotiator left a gaping hole in what she considered her calling in life, it was better than nothing, and since she was more of less confined to the city, it gave her some purpose.

John Sheppard however was having a much rougher day, having been called into Colonel Carter's office for the one reason he had been dreading since declaring his feelings for Elizabeth. Carter, bless her cotton socks actually looked as though she were dreading this meeting herself, her calm demeanour although professional, seemed almost to the point of rigid. She'd been on the receiving end of the very stick she was about to wield, and hated it even more so now.

Sheppard tapped on the door frame with his knuckles to gain her attention, still not quite used to see Carter seated behind the desk he had always known as Elizabeths'.

" You wanted to see me Colonel?" He asked, leaning casually against the door frame.

" Take a seat Colonel " Carter gestured towards the empty chair facing her desk, then laced her fingers together to keep from fidgeting in frustration. Sam sucked in a deep breath and braced herself for the hostile reaction she was likely to receive from her words.

" John, there's no polite way of saying thing so I'm just gonna come out and say it. Are you having a relationship with Dr Weir?" She asked, keeping her tone as even as possible.

The colour drained from John's face as her words hit home, his expression changing instantly from casual to guarded.

" With all due respect Colonel, what does that have to do with you?" John replied, unable to keep the tension from his voice.

Sam controlled her expression and kept it neutral.

" I need to know John, because if this base is ever compromised or if the dampening field McKay's rigged ever fails, her nanites may give away our location, or worse, they could take control of her. The IOA has raised some concerns as to what the 'failsafe' plan is going to be." Carter explained, trying to put the words into a manner that didn't put her into the category of heartless bitch.

" And you want to know if I'm in a relationship with her... because of that?" John questioned incredulously, his eyebrows rising in a way very similar to Elizabeth's.

" I need to know if it's gonna be a problem for you if she's put into stasis or..... deactivated if it comes to that" Sam said with more than a little regret in her voice.

John kept silent for a moment, digesting the new information and carefully choosing his words

" I have never, and will never, let any personal relationship I have interfere with my duties Ma'am. But with regards to Elizabeth, she is no longer my commanding officer, nor is she a member of the military, so there's no regulation to say that we CAN'T have a relationship" John answered, hoping that that was the answer Carter was looking for.

Sam sucked in a deep breath, knowing he was trying to play the company tag line and sprout what she wanted to hear.

" John... you're the closest one to her, so if the worst does happen, and she is compromised or action needs to be taken, you're most likely gonna have to be the one to do it" Sam regretted her words the instant she was forced to say them " I need to know if that's gonna be a problem"

John bristled at the thought of having to hit the literal 'kill switch' that would deactivate Elizabeth's nanites and essentially kill her instantly, the stasis option however he could handle.

He resisted the urge to jump to his feet and defend against Elizabeth being treated like an unpredictable machine, it was hard to do but he knew that making a scene would only make things worse.

" What are the markers going to be if this 'plan' has to be enabled?" John asked, his tone low and barely civil.

" We're still putting it down on paper, and it's something that Elizabeth will be made aware of in the near future, but she will be put into immediate stasis if any of the following occur a) the dampening field that McKay rigged fails or is on the verge of failing, b) if any replicators are in the immediate area, we still don't know how effective that field is short range or c) if the city is under heavy attack or taking damage. To that end, the discussions as to what will happen if we're forced to evacuate are still ongoing, she can't come back to Earth for obvious reasons...and we can't leave her hear for someone else to find her" Sam's voice drifted off, leaving John to know exactly what the 'resolution' to that situation would be.

John couldn't resist the urge to stand and start pacing, thankful the glass doors to Carter's office had closed behind him when he'd originally entered.

" I'm sorry but I'm having issues with the IOA treating Elizabeth like a liability" John retorted angrily, his posture radiating anger and frustration. " We're talking about Dr Elizabeth Weir.. the same woman who headed up this expedition for 3 years and was your boss for a time back at the SGC!"

" I know John, but the...failsafe... needs to be clear for all concerned before the situation arrises and needs to be dealt with" Sam explained, keeping her tone calm, if not a little apologetic.

" When are you going to tell Elizabeth about this little failsafe plan?" John snapped back before taking a few mental steps to reign in his anger.

" Once it's down on paper and has the President's approval." Carter replied and noted that the mention of the President seemed to sooth John's ire a little. " We are being as delicate as possible about this John, it's being given every consideration by the highest levels"

" I know... it's just.... she's not a machine that can be switched off on a whim. We flick that switch we kill her" John replied with irritation, his eyes flashing with emotion.

" I know John, but if the worst situation comes.. it may be necessary" Sam said softly " Which is why we plan on using the stasis chamber you found her duplicate in 3 years ago for all except the more dire"

" I see " John returned, slowing his pacing and nailing Carter with a glare that could be interpreted many ways. " You have my word Colonel that when the time comes, the appropriate actions will be taken" He saluted stiffly before stalking out of her office, not even looking where he was going until his feet seemed to deliver him to the door of another office, Elizabeth's new office.

She looked up as she noticed him though the glass door, a concerned expression on his face and his entire body radiating tension.

" John... come in. What's wrong?" She asked, concern causing her eyebrows to knit together. He had that look about him that something horrible had happened and he was struggling to deal with it.

" I just got called into a meeting with Carter... she wanted to know if there was an 'US'" He said solemnly, hoisting his hip onto the corner of her desk as he did so many times back when she was in charge.

" I see" Elizabeth replied, her expression also a little guarded, she was bracing herself inwardly " And what did you say?"

" I told her the truth, and that we wouldn't let it interfere with our duties" He retorted, his voice all singsong like he was a school child reciting the school motto.

" And she was ok with that?" Elizabeth asked, her expression still guarded.

" There's nothing she can do in relation to regulations anyways... and I think she kinda knows how we feel if you know what I mean" John smirked, trying to lighten the mood so Elizabeth didn't delve deeper into his discussion with Sam. He didn't want to reveal the details of the failsafe, ever preferably. But in the meantime it would need to be approved by the President before it was even mentioned to Elizabeth. And while it pained him to keep such information from her, he knew that he had little control over Sam's orders. Elizabeth wasn't to know... not yet. Regardless, Elizabeth still knew the reality when it came to her nanites, and what that may mean for her future, she could handle the truth when the time came, that he was sure of.


	5. Chapter 5

It was less than a day later before the situation John Sheppard had been fearing came to pass, and he was forced to face his nightmare. He'd spoken to Rodney McKay later the previous evening and all but ordered him to find a way to completely neutralise Elizabeth's nanites so she wouldn't have to be put into stasis or worse yet deactivated. On his way out of the science lab he'd bumped in Dr Zalenka and brusquely ordered him to double check the stasis chamber was ready to be powered up at a moments notice.

" But why?" Radek started to protest, his voice thick with his accent.

" Just do it" Sheppard snapped and stalked out of the lab, leaving too rather frazzled scientists in his wake. He'd taken himself for a run to drain the aggression from his body, his entire body screaming for a reprieve before he slowed his pace even a fraction. The city was bathed in darkness, suiting his mood and hiding his drawn features from the other members of the expedition. Soft lighting illuminated the sections of hallway and piers as he passed, returning to darkness as soon as he'd moved on, conserving power.

It had been in the wee hours of the morning that the city shuddered from the assault from space, lights dimming as power was routed away from non-essential systems and into the shields. John tumbled out of bed and was out the door even before he'd had a chance to lace his boots up properly, heading towards the control room to see what was going on.

He nearly ran into a pylon as the city shook from another hit, bracing himself with his arms before pushing off and continuing on his flight.

" What's going on?" He puffed as he skidded into the control room, the area a flurry of frenzied activity as key personnel struggled to keep up with the attack.

" It's a Replicator ship, we think they've picked up the signal from Elizabeth's nanites and are investigating" Carter explained, gripping a consol as the city shuddered again.

" Are you sure?" John asked, a sinking feeling in his gut. If the Replicator's had found Elizabeth, then he would be forced to.... no he wasn't going there just yet, there had to be an alternative.

" No.. but they're Replicators and they're here... 2 and 2 still equals 4" Rodney retorted angrily as his fingers danced over the keyboard of his laptop.

" Did you have a chance to look into Elizabeth's nanites?" John questioned, nailing Rodney with an accusing glare that made the stubborn scientist actually pale.

" No....but now I know why....If you get her into the stasis chamber it should neutralise any nanite activity" Rodney said quickly, his eyes wide with recognition. " We haven't tested the stasis chamber since... you know.. the other Elizabeth so I don't know if its working properly, and there's no time..." His words were cut off as the city shook violently again.

Dr Elizabeth Weir was nearly shaken out of bed as the city rocked beneath her, waking her up more efficiently than any strong coffee could. Quickly changing out of her night clothes and into her regular uniform she tugged on her boots and headed up to the control room out of habit, not realising she wasn't really required there anymore.

As she emerged in the control room an eerie silence fell over those gathered there, making her wonder what exactly was being heatedly discussed before her presence was noticed. Any words were cut off as John grabbed her wrist, pulling her back the way she'd come.

" Elizabeth... you've got to come with me. Have Zalenka meet us in the Stasis Room" He said stoically as he half jogged half ran down the corridor with her in tow. She saw Carter's face fall and Rodney's head in his hands as she turned.

" John, what's going on?" Elizabeth shouted over the din, the confusion on her face evident as she was half pulled half dragged through the corridor.

" We need to put you in stasis...the Replicators may be trying to find you" John replied, slowing his pace just a little as the corridor became crowded.

Realisation dawned on Elizabeth " You're trying to protect me...to protect yourselves" she started, gripped John as the city shuddered again.

" It's either this or Rodney tries the kill-switch again, and that's one option we are NOT exploring" John retorted angrily, picking up the pace again as the people thinned.

Within a few minutes they'd arrived at the stasis room, Dr Zalenka waiting anxiously for them as they entered. He looked disheartened by what he had to do, but knew there was no avoiding it. Elizabeth hesitated as she saw the chamber again, causing John to turn and release her wrist.

" Elizabeth… it's the only way" John insisted, not voicing the alternative again. Thankfully Radek had the nous not to voice his own concerns about the lack of testing and analysis on the stasis chamber. There was a naquedah generator attached to the controls in the centre of the room, quietly humming away as it provided a power source the Replicators couldn't take down with their weapons.

" Just in case the shields fail... or we lose power… this should keep the stasis chamber going long enough to someone to get down here and reanimate you" Radek explained quickly, his accent making it hard to understand the exact words.

" It's ok Radek..." Elizabeth said quietly, giving him a look that conveyed her acceptance. She always knew there would be an issue with the nanites if they were never completely neutralised. This was the price she would pay for the chance to live again. John released the grip he had on her wrist, his eyes speaking an apology that words could not explain. She simply nodded and stepped towards the chamber, wondering what it would feel like to be put into stasis.

" Everything seems ready" Radek lamented as though he wished there were another alternative.

" Elizabeth I...." John started, before a finger on his lips stopped him. The finger was replaced by a featherlike kiss, a kiss that promised more should the situation allow it. She broke the contact to see a very red faced and embarrassed Zalenka trying very hard to look anywhere but at the two of them. Without a word she stepped into the chamber and turned to face them, John's anguished face and Radek's sombre expression the last things she saw before the world faded to black around her.

" The system looks stable" Radek noted as he checked and rechecked the stasis chamber's systems. The naquedah generator supplemented the power source and was functioning efficiently, allowing him to breathe a small sigh of relief.

" Nanite transmissions falling….. " Rodney's voice echoed around the quiet chamber as he patched himself through the communications system into the room.

" Thank God" Radek sagged in relief, relinquishing his death grip on the controls. John had vanished to the chair room as soon as Elizabeth was 'secure', leaving Radek feeling very much alone.

It took a short time but the weapons fire seemed to slow as well, as though the Replicators were trying to figure out why the transmissions stopped. They lingered for several hours longer, taking the occasional pot-shot before leaving the area entirely, allowing everyone in the city to relax finally.

John emerged from the chair room looking drained both emotionally and physically, his complexion pale in comparison to the shock of black untameable hair he sported. He made his way to the control room to see Carter in deep discussion with McKay, neither looking very pleased with whatever it was they were talking about.

" We can't keep her in there forever" Rodney was protesting, his hands animating his frustration.

" We can't let her out with the nanites still transmitting… It'll bring the Replicators back here in a heartbeat" Carter implored, her expression sympathetic but firm.

" I….. I just need some time to figure something out" Rodney stuttered, his hands already beginning to tap away at his laptop.

John caught the tail end of the discussion and motioned Carter towards Elizabeth's old office. She nodded towards McKay and left him to work.

Once the doors closed behind them John couldn't hold his anger back any longer.

" You're planning on leaving her in there aren't you?" He exploded, his tone the barest inkling away from insubordination.

Carter sucked in a deep breath as though she had been expecting this confrontation, schooling any irritation away from her features and keeping her expression neutral.

" I plan on keeping her in stasis until McKay can permanently disable her nanites… yes." Sam explained carefully, hoping that Sheppard would see her point of view.

" Was that the plan all along?" John accused, his face dark with anger.

" No. It wasn't until the Replicators arrived to check out the nanite transmission did we realise the gravity of the situation. The dampening field obviously hadn't worked like we'd hoped. When Rodney works out a way to neutralise that transmission and the nanites for good, she'll be released. Not before. We can't risk it" Carter plonked herself behind her desk and regarded John with a commanding gaze. She understood his frustration, heck she felt it herself, but the wellbeing of the city and the expedition was her primary concern just as it had been Elizabeth's. The needs of the many had to outweigh the needs of the one.

" I know why you did it, I just don't like it" John finally calmed, his expression changing from one of anger to one of resignation.

" I understand John, but it's up to the scientists now. As soon as they can sort out the nanites, everything will be resolved. Until then... she stays in stasis." Sam finished, putting an end to the discussion and any rebuttal John may have been thinking of.

He hesitated a few moments before a crisp " Yes Ma'am" and stalking out of her office.

Much to his chagrin the repairs to the city kept him occupied for a number of hours, it also gave the scientists a small headstart before he could start nagging them for progress. After a drive-by the science labs to check on their progress later that evening John finally ended up in the stasis chamber, his feet having had a mind of their own and taken him there as his mind stewed over the possibilities of never seeing Elizabeth alive again.

She looked so peaceful encased within the stasis chamber, her eyes gently closed and the glass slightly opaque to indicate the chamber was indeed working. John's heart clenched in anguish, seeing her so peaceful and so close, yet so untouchable.

How long would she be forced to remain like that? His hand reached to touch the glass, the fingertips tracing the line of her jaw through the frosted material. He felt so terribly alone in the universe at that moment, cut off from the one person he drew strength and courage from. Could he go through losing her a second time?


	6. Chapter 6

Four months later Dr Rodney McKay finally thought he had made some headway in neutralising Elizabeth's nanites. He'd worked almost non-stop on the project, pausing only for meals of the most essential nature (which for him was 5 a day), and to grab a few hours sleep in between the usual crisis that seemed to plague Atlantis. The Replicaters had returned numerous times during the time since Elizabeth had been put into stasis, searching for the nanite transmissions they had picked up previously. Whilst the city had been able to fend them off on each occasion, the Replicators learnt from each encounter, trying different tactics to get through the Lantean shield. It wouldn't be long before they worked out how to penetrate the shield altogether, and that was a situation Rodney didn't want to deal with.

He ran a simulation for the 15th time, checking and rechecking the results before calling Colonel Sheppard and Colonel Carter into a meeting to share his theory. When they wandered into his lab, both looking drained from the most recent Replicator attack, his head snapped up in surprise.

" Oww.... how'd you get here so quick?" He complained, rubbing the back of his neck to ease the muscle cramps there.

" We were in the area, now what have you got?" Sheppard snapped, getting straight to the point. Everyone had noticed the change in his behaviours and moods since Elizabeth had gone into stasis. He'd become withdrawn and isolated, still doing his job, but not with the same zeal as before.

" The Holy Grail" Rodney said simply, turning his laptop around so that Sam Carter could see the horribly complex series of algorithms and coding displayed on the screen.

" You plan on unbinding the nanites from Elizabeth's cells.... then turning her into a carrier for a new Replicator virus?" Sam asked incredulously, glancing up from the laptop to see Rodney's smug expression.

" Won't that kill her... unbinding the nanites?" John asked, doubt still seeded within his voice.. how often had they gone down this path within the last few months only to hit a brick wall?

" Not if I tell them to replace the nanite portions of her brain with organic replicants of the original tissue, BEFORE they unbind" Rodney continued., pulling up a fairly complex diagram that would hopefully make it a little easier to explain.

" They can DO that?" John queried, raising an eyebrow in a very 'Elizabeth' gesture.

" They can when I program them to... but that's not the best of it" Rodney kept on at a million miles an hour, his hands dancing expressively before him. " The Replicator virus I've created will do the same for all Replicators, cause them to unbind and become uncohesive. They'll just fall apart!" He said gleefully, his expression one of utter smugness.

John fought the urge to slap him, mainly for Carter's sake and settled for a deadly glare.

" And just how do you plan on transmitting this 'virus' to the Replicators?" John asked, not liking where this discussion was heading.

" That's where Elizabeth comes in... she'll transmit the virus next time the Replicators come back" Rodney replied, his enthusiasm dying a little.

" You plan on turning her into a Typhoid Mary?" John gasped, his mouth agape as he tried to understand " This is ELIZABETH we're talking about"

" I know, but if we can bring her out of stasis and reprogram her nanites, and 'allow' the Replicators into the city, they link with her and wooshka.. they all fall apart" Rodney's zeal lessened again as he recalled the last time a Replicator had probed his mind, it hadn't been a pleasant experience then and was more than likely going to be worse for Elizabeth. Unfortunately she wasn't around to be asked.

John seethed, his anger visible on his features as he paced the room like a caged animal. How could Rodney want to USE Elizabeth like that... use her as bait! Deep down he knew she would agree to the plan if it gave Atlantis such a weapon against the Replicators, but still, he hated to see her in harms way. What if they noticed her nanite's had been altered before they linked with her?

" I can't believe you want to use Elizabeth as bait.. can't there be any other way to 'uploading' this virus?" John glared at the withering scientist, his eyes blazing with fury.

" Well we can't exactly go back to the Replicator Homeworld... we needed Elizabeth for that last time and look what that cost us" Rodney retorted, a pleading glance directed towards Carter for support.

" John... " Sam said cautiously, not wanting to anger him further but needing to gain control of the situation. " This is my call"

" Thank you" Rodney said in a small voice, unconsciously moving towards Sam and away from the still seething John.

" And what's your call?" John snarled, resuming his pacing. Every fibre of his being was against the idea, his job had always been to protect Elizabeth, not put her willingly in danger and potentially back into the hands of the Enemy. His feelings for her had only deepened in the time she'd been in stasis and he rebelled against the idea of potentially having her back only to lose her again.

" I say we do it. From what I know of Dr Weir she would want us to take out the Replicators by any means necessary. If it goes to plan its a win/win situation, we'll just have to make sure it goes to plan" Sam said carefully, nailing John with a look that spoke a thousand words. He took the hint and backed off, settling for looking rather grumpy.

" How long will it take to set up?" Sam asked McKay, who'd somehow ended up behind her left shoulder. She turned on her heel to face him.

" Umm... it's set up... I just have to take Elizabeth out of stasis, and upload the virus into her nanites, then we wait till the Replicators show up." Rodney explained, pointing towards the laptop as if to show that he actually hadn't been wasting time.

" Get to it" Carter ordered before turning and leaving the lab, a hidden smirk on her face at Rodney's miserable expression. The scientist scrambled to retrieve his laptop and scurried out of the room, a still seething John tailing behind him.

A short time later they were in the stasis room, Zalenka and Dr Keller having joined them in case there were any complications. Four marines stood by the door, each carrying a ARG in case anything unexpected should occur. John was thankful for their presence but loathed it at the same time. If they fired before the Nanites finished their new programming.. Elizabeth would be dead as sure as if she were shot with a P90.

Rodney looked toward Sheppard as he finished setting up his equipment, the question as to wether he should proceed despite Carter's approval clearly on his face.

" Do it" John grumbled, not taking his eyes of Elizabeth behind the frosted glass. He had made it a daily vigil since she'd been put in that chamber, to come and visit her, telling her about the daily goings on in Atlantis despite the fact he knew she couldn't hear him. Something about her mere presence, even in stasis calmed him.

The marines stepped forward to the front of the small congregation, ARG weapons raised and ready to fire. While Elizabeth had remained in control of her nanites in the time since she had been recovered, there was still a chance they would take control of her once again.

" Ok… releasing the stasis field…. NOW" Rodney remarked as he toggled the appropriate control on the panel before him. It took a few moments for the system to revive her, the frosted glass losing its opaqueness as she returned once more to life.

The door hissed open and she stepped out, a look of utter confusion on her face as the ARG's were aimed directly at her.

" What's going on?" Elizabeth asked, looking around the room with a touch of fear in her eyes. This was not what she had expected when she'd been put into stasis.

" Rodney's gonna reprogram your nanites and then use you as bait to lure the Replicators here... then you'll infect them" John said simply, his eyes pleading with her to go along with the plan.

" Ok… what do you need me to do?" She asked quietly, her expression one of trust.

" Just stand there for the time being… I should be able to upload the program remotely… and…. THERE" Rodney pressed a series of buttons on his laptop and glanced towards Elizabeth. " How do you feel?" He asked, waiting the colour drain from her face with each passing moment.

" I…" Her voice failed as she collapsed in a tangle of limbs, John's strong arms catching her before she hit the deck. He eased her gently onto the floor and pushed the marine's aside to make room for Keller.

" Doc?" He asked after a few moments, anxious to know what was going on.

" It's ok John" Jennifer said as she completed another scan " The Replicators are rebuilding portions of her brain with organic tissue…we need to get her to the infirmary though, I want to keep an eye on her"

John breathed a sigh of relief before scooping Elizabeth up in his arms, heading towards the door with the Marines, scientists and Dr Keller in tow. He'd gotten no more than two corridors towards the Infirmary when the city shook with an eerily familiar blast.

The Replicators were back… and had been hiding just out of sensor range until Elizabeth had been reanimated. This time they were getting what they came for.


	7. Chapter 7

The city shuddered beneath John's feet as he sprinted towards the infirmary, a trail of medics and military personnel on his tail as he ran. It took far to long in his opinion to get there and as he did he laid Elizabeth out on the first available bed whilst Dr Keller hurried to get the scanner hooked up and in position.

" Carter to Sheppard, the shield's weakening, looks like they're adapting, I don't know how long its gonna last" Her voice was calm but conveyed a sense of urgency John had rarely heard from her before. So much was riding on Elizabeth, for an instant he thought it may be too much.

The scanner hummed to live, descending slowly along Elizabeth's body and displaying the detailed images on a nearby computer screen. Slowly but surely the Nanites within Elizabeth's body were rebuilding her brain as well as the other parts of her body they had used themselves to repair previously, this time they were creating organic components, components that couldn't be harmed by the virus that would kick in at any tick of the clock.

" How is she Doc?" Sheppard asked anxiously, hating the fact that seeing Elizabeth pale and unconscious reminded him of when the nanites tried to overtake her body the first time around. How long ago had that been now? It felt like a lifetime but he pinned the exact number to the day in his mind. If this worked, he would have Elizabeth back as whole as she had been before Niam had attacked her. Still, he couldn't get his hopes up just yet, they'd been dashed before.

" The nanites are rebuilding her brain as we speak, it'll take some time before she's conscious though" Keller announced from her position in front of the monitor. She looked at another monitor which displayed Elizabeth's vital signs, they fluctuated as her body dealt with the changes being made, her blood pressure and neural activity spiking periodically.

The next blast nearly through them off their feet, the impact far worse than anything they had felt so far. The shield had been breached and soon Replicators would flood the city in their search for Elizabeth.

" Shields have collapsed, all personnel report to defensive positions" Carter's clear voice rang through the corridors, causing a stir of activity. Weapons were drawn and checked, scientists barricaded themselves in their labs, and the infirmary prepared itself to the usual inundation of patients that usually came from the cities defences being breached. John however stepped forward.

" Clear the room of all but essential personnel, set up your triage in the Mess Hall" he ordered, causing a worried look from Keller.

" We can't just up and leave, there are patients here who need…" She started, only to be cut off by Colonel Sheppard.

" They're here for Elizabeth, the more people in the way, the more people get hurt" John replied, his tone low and lethal.

" Sam, the way to get out of this with the least amount of bloodshed is to let them into the city, and clear a path to the Infirmary, they're after Elizabeth first up" John explained through his earpiece to Sam, who clung to her consol as the city trembled beneath her feet.

" Are you saying we LET them have her?" Sam questioned, her tone uncertain as chaos reigned supreme in the control room.

" It's the only way to get out of this with the city and most of us intact" John replied quickly, steadying himself on Elizabeth's bed as the deck bucked.

" Alright… I hope you're right on this John" Sam signed off and sent another announcement through the military personnel's com pieces advising them of the change. They were not to approach the Replicators unless they were directly being threatened.

Before long a small army of Replicators emerged into the corridors of Atlantis, only to find the majority of the expedition nowhere to be seen, or if they were around, non-confrontational. It didn't take them long to narrow the location of the one who had escaped and to close in her position.

Sickbay was all but deserted when the small number of Replicators cautiously entered, carefully looking for any traps or hidden attacks that might be sprung upon them. John stood alone beside Elizabeth, his ARG lowered but his finger still on the trigger.

" We have come for her" The lead Replicator announced without emotion.

" I know" John replied, his weapon still lowered.

They advanced until the lead Replicator was level with Elizabeth's bed, opposite John and regarding them both carefully. This lack of confrontation confused them greatly, they had anticipated much resistance.

His hand raised and approached Elizabeth's forehead, causing John to raise his weapon.

" I won't let you take her" He threatened, his voice barely above a whisper in the silence.

" She is one of us, and will be returned to us" The Replicator intoned, as though he were explaining the complexities of the colour grey to someone who was colourblind.

" Like hell she will be" John retorted, his finger itching to pull the trigger. He knew at this critical juncture the Replicators mustn't catch on to the ruse, if they did, all would be lost. He deliberately stepped forward in front of the nearest Replicator, a stupid move that no military officer worth his stripes would ever do but knowing he had to keep the ruse going. As predicted they retaliated, sending him reeling into the bed next to Elizabeth's. The impact left him groggy and disorientated, unable to control his own movements as the sound of screaming hammered his ears.

Not just any screaming… Elizabeth's.

He cracked open an eye to see her writhing on the bed, the Replicator's hand deeply embedded within her forehead. They were probing her mind, trying to learn what she had accomplished since they had noticed she was missing.

The look of shock crossed their faces simultaneously, followed by the inevitable look of defeat as the virus was uploaded into their bodies. A moment later they all fell into a pile of silver dust on the floor, the sound not unlike the raining of marbles from a small height.

Dr Keller emerged from behind one of the patient partitions, a look of fear mixed with relief on her face. She tentatively made her way to Elizabeth's side, checking the other woman's vitals whilst trying not to step in the pile of dust that was the Replicators.

John groaned from his uncomfortable position, slowly regaining control of his mind and muscles. He pulled himself upright and leant on the bed for support.

" Is she ok?" He asked, his voice thick with concern.

" She appears to be, the nanites have finished repairing her brain and uncoupled, they're still in her bloodstream but now 100% inert. It'll probably take her a while to get back to normal though, she's been through a lot" Keller explained, having finished with Elizabeth and making her way over to John. " How are you doing?"

" Next question" He grumbled, struggling to hoist himself back onto the bed. Truth be told he hurt like hell and the blood curdling scream still echoed in his ears.

Keller gently pushed him back onto the bed, unzipping his tactical vest and pushing it aside to better examine his torso. From what she could see he was badly winded and would be sporting a large bruise for some time, but was otherwise relatively uninjured.

The next two days for John were spent in the Infirmary, mostly in a chair pulled up by Elizabeth's bed once he was released from his own by Keller. Everyone came to visit, even Rodney who stood there in a rather awkward silence until his brilliant mind tried to form some kind of sympathetic coherent thought.

Elizabeth thought she was alone when consciousness finally decided to grace her with its presence. She could hear the muted shuffling of the medical staff nearby, coupled with the steady rhythm of a heart rate monitor. A slight pressure on her index finger signified a blood oxygen monitor as well, it was cumbersome as she tried to experimentally wiggle her fingers, remembering the sensation from what seemed like so long ago.

" Hey…good to see you awake" Came the quiet voice of Jennifer Keller, glancing from Elizabeth to the monitors that were displaying her vital signs. Elizabeth cracked open her eyes and blinked to clear the fuzziness from them. Her gaze fell upon a shaggy mop of untameable black hair buried in the crook of a black clad arm, obviously asleep.

" Has he…?" Elizabeth asked, already knowing the answer to her question.

" No, he hasn't moved, and its good to see him finally getting some rest, although its not the most ergonomically sound position" Keller said gently, keeping her voice down so as to not disturb John. Elizabeth however had other ideas, raising a weak arm to gently ruffle his hair, a tender touch with more meaning than either would care to admit. John's head snapped up at the contact, his eyes confused for a moment before taking in the very much alive and awake woman before him.

" You're awake…" He stated groggily as his mind cleared itself from the lingering fog of sleep.

" It seems that way " Elizabeth remarked, holding the contact with his eyes as long as she could without seeming overly obvious. " Mind filling in the gaps? I'm still a little confused how I got here…"

John sucked in a breath before leaning back in his chair. " Do you remember being put into stasis?" He questioned.

" Yeah, feels like yesterday" She replied, rubbing her forehead with the hand not attached to any IV lines or monitoring equipment.

" It was months ago. It took Rodney that long to come up with a way to get rid of those nanites inside you once and for all, as well as coming up with a rather genius plan – even by my standards – to take out the Replicators for good." John started, pausing for a moment for Elizabeth to digest the information.

" Problem was, the Replicators were looking for you, and keep attacking the city trying to find you. To get this plan to work we had to take you out of stasis, reprogram your nanites, then use you as a lure to bring them here. They tried to probe your mind and got infected with the virus Rodney created, and Bingo, no more Replicators" he finished, making a point not to mention the sight of her writhing in agony or the way her screams would stay with him for the rest of his life.

" I see" Elizabeth said simply, processing the information at her own pace. She would ask him more later when she didn't feel like she would fall asleep on the spot. She rested her head back on the pillows, her eyes closing of their own accord as her energy reserves bottomed out.

Dr Keller checked her vitals again to find her resting this time, falling gently into a deep healing sleep. She saw the question in John's eyes " She's just sleeping, it'll take a while before she's back on her feet" She put his mind at ease. " And _you_ should get some sleep too, the next bed's free if you want to crash out there"

" Yes Boss" he grumbled, easing himself out of the chair and hoisting himself on the bed, unlacing his boots and pulling off his vest before curling up on the bed, instantly asleep.

A week later Elizabeth was finally released from the Infirmary, given a clean bill of health and completely free from nanites. A innovative therapy devised by Rodney and Dr Keller had removed the inert nanites from her bloodstream, not that she was awake enough to know how they did it. That week had been spent in a haze of semi-conscious sleep and increasing amount of alertness. John had filled in most of the gaps in her memory and she revelled in the fact that she had played a rather substantial roll in ridding the galaxy of one of its scourges. Not that the victory would last long, they never did in the Pegasus Galaxy.

The next day she was summonsed to Carter's office… 'her old office' she mused to herself as she dressed in casual clothes that morning. John had given her breakfast in bed before leaving to go about his duties, letting Elizabeth get ready in her own time. She could sense something was going on but no-one was letting on, going about their business with an oddly familiar look on their faces.

She knocked on the doorframe of her old office and saw Sam's head rise from the report she was engrossed in.

" Dr Weir, it's good to see you up and about" Carter said pleasantly, gesturing to a vacant chair on the opposite of her desk. Elizabeth plonked herself in the offered chair, realising how weird it felt to be sitting on this side of the table.

" You wanted to see me?" She asked, rising an eyebrow at Sam's small mountain of reports awaiting approval.

" I did… I've informed the IOA of your progress and recovery" Sam started without preamble. Interlacing her fingers and setting her hands on the table.

" I see" Elizabeth replied, not sure where Sam was going with this rather abrupt start to the conversation.

" They want you back as leader of Atlantis, when you're ready to take it on again, I'm apparently needed more back on Earth" Carter explained, obviously not happy with the whole idea. Atlantis was the dream posting of any miliary or civilian personnel, and it hurt to be recalled away from it at such short notice. " There's a catch though, Mr Woolsey will be here as an overseer for the first 6 months, just to make sure you're still as he put it 'Right for the job' "

Elizabeth stayed silent for a moment, unable to come to terms with the fact that she was once again put back in charge of such an expedition. The glory was tempered with the bittersweet though of Woolsey being a constant thorn in her side for the next six months.

" I'm sorry to hear you've been recalled to Earth, from what I hear you have done a wonderful job here" Elizabeth said diplomatically, nodding her head towards Sam in a gesture of respect.

" I did what I could, I can't say it was ever easy" Sam replied, leaning back in her chair. The silence seemed to engulf them as they each got caught up in their thoughts.

" I'm sorry, I shouldn't keep you from your work" Elizabeth stood, ready to excuse herself from the office that would soon be hers.

" Think nothing of it, I needed the break." Sam rubbed her eyes with the back of her hand. She looked tired, as though the last several months had taken their toll on her. She had proven herself here on Atlantis as a strong and capable leader, but as she had admitted, it hadn't been easy. "Congratulations Dr Weir" Sam extended her hand.

" Thank you, and thanks for keeping this place in one piece, its not a mean feat these days" Elizabeth quipped, shacking Sam's hand before letting herself out of the office.

Her feet took her to her favourite balcony as her mind processing the good news, she leant against the railing, enjoying the feel of the breeze in her hair and the scent of salt in the air. Inhaling deeply she closed her eyes and savoured the sensation, wondering how quickly she had forgotten the peace and tranquillity this balcony had always provided.

" I see Carter told you the news?" A voice came from behind her, and she grinned in reaction.

" You knew" She stated simply, twisting to see him emerging from behind one of the pillars with a lopsided grin on his face.

" It was hell keeping it from you, but Carter wanted it to be a surprise" John remarked, settling in behind her and wrapping his arms around her protectively.

"So that's why Rodney's been grinning like an idiot for the last two days" Elizabeth quipped, resting her head back against the strong chest behind her.

"That would be it, poor Rodney's never been good with secrets, but I must admit its remarkable what the threat of slipping a lemon into all the food in the galley can accomplish" He smirked, giving her a little squeeze to prove his point of victory.

Elizabeth bit back a retort but decided against it, sometimes it was good to see the brilliant scientist taken down a peg or two. She enjoyed the warmth of John's body pressed against hers, the breeze still ruffling her hair and his chin now resting on her shoulder.

" This is nice" She sighed in contentment, laying her hands over his as they encircled her waist.

" It is, its nice to have you back, for good this time. I've missed you so much" John admitted, the level of sentiment unusual even from him.

" It's good to be back" Elizabeth whispered, giving his hands a squeeze.

For once, the Pegasus Galaxy seemed to be giving them a break for a change. How long it would last, no-one knew, but right at that instant, she was the happiest woman in the galaxy, nestled in the arms of the happiest man.

The End


End file.
